As some of you may already be aware, we have begun construction of a new forum as a rebirth of PHO and continuing on into future projects.
This forum is called Silph Co., and can be found by clicking the banner below. We are in the process of transferring some of our old resources, and the forum is open for posting. It will be sad to see PHO go, but we look forward to a bright future with Silph.
The forums here will be moved to an archive, and the url will redirect to the new site in the coming days/weeks.

1) I've actually been trying to figure this one out too, and unfortunately haven't found a definitive answer yet. So far the closest I can get is to lower the catch rate in YAPE as far down as it can go (either 1 or 0 I think) but no matter how low it gets, a Master Ball can still be used though.
_____

2) Check to make sure that the grass tile you are using is the exact same tile with the same index number as the ones that are usually used on encounter maps. I think there are probably some grass tiles in the games that don't hold encounter triggering data, and are just for decoration. If this doesn't work, make sure that the encounter percentage slider in Advance Map is on a percent above 0. Many grass maps seem to use 7%, if I recall correctly.
_____

3) In order to give additional moves to Pokémon in YAPE, apparently you must first remove some attacks from other Pokémon to make room for the new ones. For example, deleting Growl from Lapras so that you will be allowed to add Bite to Magikarp's move list.
_____

4) As far as I can tell, stat gains in the game are dependent on the game's engine itself, so you may not be able to change the rates for a specific Pokémon. I may be wrong about this though, but I've never seen anyone manage to do this before. Maybe ASM hacking could accomplish this though.

Otherwise, the closest thing I can think of to do this would be to use YAPE (or another good editing program) to simply change the base stats of the evolutions of that Pokémon. Steelix, for example is always slower than an Onix of the same level, you can do this same thing in YAPE by changing the base stats.